pipeline-atacseqlisted

# ENCODE ATAC-seq Pipeline ## When to Use - User wants to run an ATAC-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ATAC-seq pipeline", "Tn5 shift", "chromatin accessibility pipeline", or "Bowtie2 for ATAC" - User needs to process ATAC-seq data with proper Tn5 insertion site correction - Example queries: "process my ATAC-seq FASTQs", "run ENCODE ATAC-seq pipeline", "call accessibility peaks from ATAC-seq" Execute the ENCODE ATAC-seq processing pipeline from raw FASTQ files through Tn5 offset correction, peak calling, IDR analysis, and signal track generation. This skill provides a Nextflow DSL2 implementation following ENCODE uniform analysis standards. TSS enrichment scoring is a **manual post-processing step**; the workflow does not compute it (see "Manual QC steps" below and `references/05-qc-metrics.md`). ## Overview ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) uses the Tn5 transposase to probe open chromatin regions. This pipeline processes ATAC-seq data through quality control, alignment with Bowtie2, mitochondrial read removal, duplicate removal, Tn5 insertion site correction (+4/-5 bp offset), blacklist filtering, nucleosome-free fragment selection, MACS2 peak calling, FRiP calculation, and an IDR comparison for every pair of replicates. Key differences from ChIP-seq: Bowtie2 aligner (optimized for short fragments), Tn5 transposase shift correction, mitochondrial read filtering (chrM can be 30-80% of